[2024-01-25 18:40:05,467] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference
[2024-01-25 18:40:06,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,701] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg48306cf6-ba88-482e-be0b-aa0744ebe3da/GCF_003012345.1_ASM301234v1_genomic.fna.gz | prodigal -d GCF_003012345.1_ASM301234v1_genomic.fna/cds.fna -a GCF_003012345.1_ASM301234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:15,875] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:15,875] [INFO] Task started: HMMsearch
[2024-01-25 18:40:15,875] [INFO] Running command: hmmsearch --tblout GCF_003012345.1_ASM301234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/reference_markers.hmm GCF_003012345.1_ASM301234v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:16,098] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:16,099] [INFO] Found 6/6 markers.
[2024-01-25 18:40:16,131] [INFO] Query marker FASTA was written to GCF_003012345.1_ASM301234v1_genomic.fna/markers.fasta
[2024-01-25 18:40:16,131] [INFO] Task started: Blastn
[2024-01-25 18:40:16,131] [INFO] Running command: blastn -query GCF_003012345.1_ASM301234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/reference_markers.fasta -out GCF_003012345.1_ASM301234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:16,799] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:16,801] [INFO] Selected 26 target genomes.
[2024-01-25 18:40:16,802] [INFO] Target genome list was writen to GCF_003012345.1_ASM301234v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:16,815] [INFO] Task started: fastANI
[2024-01-25 18:40:16,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg48306cf6-ba88-482e-be0b-aa0744ebe3da/GCF_003012345.1_ASM301234v1_genomic.fna.gz --refList GCF_003012345.1_ASM301234v1_genomic.fna/target_genomes.txt --output GCF_003012345.1_ASM301234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:33,180] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:33,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:33,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:33,195] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:40:33,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:40:33,195] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	77.7881	204	1200	95	below_threshold
Halomonas lutea	strain=KCTC 12847	GCA_014651575.1	453962	453962	type	True	77.5876	199	1200	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	77.499	81	1200	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	77.4964	201	1200	95	below_threshold
Halomonas lutea	strain=DSM 23508	GCA_000378505.1	453962	453962	type	True	77.4728	194	1200	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	77.4547	143	1200	95	below_threshold
Halomonas endophytica	strain=MC28	GCA_002879615.1	2033802	2033802	type	True	77.3412	118	1200	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	77.3384	145	1200	95	below_threshold
Halomonas xianhensis	strain=CGMCC 1.6848	GCA_900113605.1	442341	442341	type	True	77.3345	191	1200	95	below_threshold
Halomonas nanhaiensis	strain=JCM 18142	GCA_003990185.1	1258546	1258546	type	True	77.3297	96	1200	95	below_threshold
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	77.3215	150	1200	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	77.2561	201	1200	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.2225	123	1200	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	77.2092	191	1200	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	77.2041	159	1200	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	77.203	198	1200	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	77.1789	146	1200	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	77.1788	201	1200	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.1514	147	1200	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.1468	145	1200	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	77.1373	189	1200	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.0747	156	1200	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	77.0221	200	1200	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	76.9008	149	1200	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_001854625.1	657387	657387	type	True	76.7286	168	1200	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_008247605.1	657387	657387	type	True	76.7178	175	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:33,197] [INFO] DFAST Taxonomy check result was written to GCF_003012345.1_ASM301234v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:33,198] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:33,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:33,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/checkm_data
[2024-01-25 18:40:33,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:33,236] [INFO] Task started: CheckM
[2024-01-25 18:40:33,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003012345.1_ASM301234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003012345.1_ASM301234v1_genomic.fna/checkm_input GCF_003012345.1_ASM301234v1_genomic.fna/checkm_result
[2024-01-25 18:41:02,856] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:02,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:02,876] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:02,876] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:02,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003012345.1_ASM301234v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:02,876] [INFO] Task started: Blastn
[2024-01-25 18:41:02,876] [INFO] Running command: blastn -query GCF_003012345.1_ASM301234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae322ffc-32f1-432d-b2c9-a28d39f0e7e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003012345.1_ASM301234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:04,097] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:04,101] [INFO] Selected 25 target genomes.
[2024-01-25 18:41:04,102] [INFO] Target genome list was writen to GCF_003012345.1_ASM301234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:04,116] [INFO] Task started: fastANI
[2024-01-25 18:41:04,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg48306cf6-ba88-482e-be0b-aa0744ebe3da/GCF_003012345.1_ASM301234v1_genomic.fna.gz --refList GCF_003012345.1_ASM301234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003012345.1_ASM301234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:20,452] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:20,465] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:20,466] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_003012345.1	s__Phytohalomonas tamaricis	100.0	1199	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Phytohalomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003206715.1	s__Salinicola peritrichatus	77.7881	204	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990195.1	s__Halomonas sp003990195	77.6593	81	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.00	98.34	0.94	0.91	3	-
GCF_000378505.1	s__Halomonas_C lutea	77.4436	196	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001648175.1	s__Halotalea alkalilenta_A	77.4417	153	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274785.1	s__Halomonas eurihalina	77.3961	136	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113605.1	s__Halomonas_C xianhensis	77.3648	189	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	96.25	96.25	0.87	0.87	2	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	77.3384	145	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000737985.1	s__Salinicola sp000737985	77.327	191	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_001937195.1	s__Salinicola socius	77.3224	179	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_003206575.1	s__Salinicola endophyticus	77.2697	200	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_003339685.1	s__Halomonas sp003339685	77.2395	95	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767635.1	s__Halomonas sp002119345	77.2384	97	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.32	98.32	0.86	0.86	2	-
GCF_014840935.1	s__Halomonas_E sp014840935	77.2256	147	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385845.1	s__Kushneria indalinina	77.216	197	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652795.1	s__Kushneria pakistanensis	77.1537	203	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155145.1	s__Kushneria konosiri	77.1511	188	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	77.1376	173	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754225.1	s__Cobetia amphilecti	77.0543	149	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_900312995.1	s__Kushneria phyllosphaerae	77.0221	200	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983445.1	s__Halomonas sp017983445	76.944	88	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008247605.1	s__Kushneria phosphatilytica	76.7178	175	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	99.98	99.98	1.00	1.00	2	-
GCA_007129225.1	s__Halomonas sp007129225	76.6278	70	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:20,468] [INFO] GTDB search result was written to GCF_003012345.1_ASM301234v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:20,469] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:20,482] [INFO] DFAST_QC result json was written to GCF_003012345.1_ASM301234v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:20,489] [INFO] DFAST_QC completed!
[2024-01-25 18:41:20,489] [INFO] Total running time: 0h1m15s